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Configuring sitemap/canonical after .htaccess rewrites?

Hi,

I just wondered if anybody could help me with a few configuration convention issues for sitemaps, canonicals and indexes etc?

I have written a website using PHP, and use an .htacces file to rewrite all .php files to .htm.
Also, had to redirect old page links to new locations, as all the page files were located in the root, now each page is located in a separate directory.

SITEMAP:
Q) Should the sitemap reference the original .php or rewritten .htm web pages?